[petsc-dev] PETSc release soon, request for input on needed fixes or enhancements

Sun Feb 28 18:23:17 CST 2016

On Sunday, February 28, 2016, Matthew Knepley <knepley at gmail.com> wrote:

> On Sun, Feb 28, 2016 at 3:12 PM, Barry Smith <bsmith at mcs.anl.gov
> <javascript:_e(%7B%7D,'cvml','bsmith at mcs.anl.gov');>> wrote:
>
>>
>>   Satish,
>>
>>    Yeah, hypre totally botched its implementation of a way to check for
>> the blas/lapack libraries. I've iterated with them several times on the
>> basic problem but they keep patching what they do, rather then discard all
>> their incorrect code and handle it simply as they should.
>
>
> I'm sure it would have worked if they had used CMake ;)
>
>
Intel compilers need only "-mkl" unless you want threaded ScaLAPACK. Works
for both shared and static linking.

I haven't tried but does "-lmkl" (plus appropriate LD_LIBRARY_PATH) not
work with shared linking?

As far as I know, static linking of MKL with non-Intel compiler is the only
hard case for build systems.

Obviously, CMake and C++11 are the only way to solve this problem :-D

Jeff

>    Matt
>
>
>>
>>    Barry
>>
>> > On Feb 28, 2016, at 3:00 PM, Satish Balay <balay at mcs.anl.gov
>> <javascript:_e(%7B%7D,'cvml','balay at mcs.anl.gov');>> wrote:
>> >
>> > Executing: cd
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/arch-linux2-c-debug/externalpackages/git.hypre/src
>> && ./configure --prefix=/opt/petsc-master_debug MAKE=/bin/gmake
>> --libdir=/opt/petsc-master_debug/lib CC="/opt/openmpi-1.10.2/bin/mpicc"
>> CFLAGS="-fPIC -g3" CXX="/opt/openmpi-1.10.2/bin/mpicxx" CXXFLAGS="-g -fPIC"
>> F90="/opt/openmpi-1.10.2/bin/mpif90" F90FLAGS="-fPIC -ffree-line-length-0
>> -g" F77="/opt/openmpi-1.10.2/bin/mpif90" FFLAGS="-fPIC -ffree-line-length-0
>> -g" FC="/opt/openmpi-1.10.2/bin/mpif90" FCFLAGS="-fPIC -ffree-line-length-0
>> -g" --with-MPI-include="/opt/openmpi-1.10.2/include" --with-MPI-lib-dirs=""
>> --with-MPI-libs=""
>> --with-blas-lib="-Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64
>> -L/opt/intel/composerxe/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_core
>> -lmkl_intel_thread -liomp5 -ldl -lpthread -lm
>> -Wl,-rpath,/opt/openmpi-1.10.2/lib -L/opt/openmpi-1.10.2/lib
>> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5
>> -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5
>> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64
>> -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64
>> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64
>> -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64
>> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64
>> -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64
>> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4
>> -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -lmpi_usempi
>> -lmpi_mpifh -lgfortran -lm -Wl,-rpath,/opt/openmpi-1.10.2/lib
>> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5
>> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64
>> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64
>> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64
>> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4
>> -lgfortran -lm -lquadmath -lm" --with-lapack-lib=" " --with-blas=no
>> --with-lapack=no --with-fmangle-blas=one-underscore
>> --with-fmangle-lapack=one-underscore --without-mli --without-fei
>> --without-superlu AR="/bin/ar cr"
>> >
>> > checking for dgemm_ in -lm... no
>> > checking for dgemm_ in -lquadmath... no
>> > checking for dgemm_ in -lm... (cached) no
>> > checking for dgemm_ in -lgfortran... no
>> > checking for dgemm_ in -linux/4.8.5... no
>> > checking for dgemm_ in -lm... (cached) no
>> > checking for dgemm_ in -lgfortran... (cached) no
>> > checking for dgemm_ in -lmpi_mpifh... no
>> > checking for dgemm_ in -lmpi_usempi... no
>> > checking for dgemm_ in -linux/4.8.5... (cached) no
>> > checking for dgemm_ in -lm... (cached) no
>> > checking for dgemm_ in -lpthread... no
>> > checking for dgemm_ in -ldl... no
>> > checking for dgemm_ in -liomp5... no
>> > checking for dgemm_ in -lmkl_intel_thread... no
>> > checking for dgemm_ in -lmkl_core... no
>> > checking for dgemm_ in -lmkl_intel_lp64... noconfigure: error:
>> **************** Non-linkable blas library error:
>> ***************************
>> >      User set BLAS library path using either --with-blas-lib=<lib>, or
>> >      --with-blas-libs=<blas_lib_base_name> and
>> --with-blas_dirs=<path-to-blas-lib>,
>> >      but -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4
>> -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64
>> -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64
>> -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64
>> -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/opt/openmpi-1.10.2/lib
>> -L/opt/intel/composerxe/mkl/lib/intel64  -lm -lquadmath -lm -lgfortran
>> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4
>> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64
>> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64
>> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64
>> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5
>> -Wl,-rpath,/opt/openmpi-1.10.2/lib -lm -lgfortran -lmpi_mpifh -lmpi_usempi
>> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4
>> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64
>> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64
>> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64
>> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5
>> -Wl,-rpath,/opt/openmpi-1.10.2/lib -lm -lpthread -ldl -liomp5
>> -lmkl_intel_thread -lmkl_core -lmkl_intel_lp64
>> -Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64  provided cannot be used.
>> See "configure --help" for usage details.
>> >
>> *****************************************************************************************
>> >
>> *******************************************************************************
>> >
>> >
>> > Hm - instead of using all the libs from --with-blas-libs in a single
>> > link command - hypre is checking one '-llibrary' form this list at a
>> > time? [including -linux/4.8.5 which is from a -L option]
>> >
>> >
>> > '-lm -lpthread -ldl -liomp5 -lmkl_intel_thread -lmkl_core
>> -lmkl_intel_lp64' ?
>> >
>> > Is hypre configure reversing the arguments it got? Its changed from
>> >
>> > --with-blas-lib='... -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread
>> -liomp5 -ldl -lpthread -lm ...'
>> >
>> > I can reproduce this issue locally with:
>> >
>> > ./configure --download-hypre PETSC_ARCH=arch-hypre
>> --with-blas-lapack-dir=/soft/com/packages/intel/15/update3/mkl
>> --with-sowing=0
>> >
>> > Satish
>> >
>> > On Sun, 28 Feb 2016, Eric Chamberland wrote:
>> >
>> >> Hi Barry,
>> >>
>> >> the configuration of hypre looks broken since last night...?
>> >>
>> >> Here is the log issued from our automatic compilation of
>> petsc-master.tar.gz
>> >> at 2016-02-28 02h00:
>> >>
>> >>
>> http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/configure_20160228_0200.log
>> >>
>> >> Everything was fine until last night...
>> >>
>> >> Thanks,
>> >>
>> >> Eric
>> >>
>> >> Le 2016-02-27 15:36, Barry Smith a écrit :
>> >>>    PETSc Users,
>> >>>
>> >>>     We are planning the PETSc release 3.7 shortly. If you know of any
>> bugs
>> >>>     that need to be fixed or enhancements added before the release
>> please
>> >>>     let us know.
>> >>>
>> >>>     You can think of the master branch of the PETSc repository
>> obtainable
>> >>>     with
>> >>>
>> >>> git clone https://bitbucket.org/petsc/petsc petsc
>> >>>
>> >>> as a release candidate for 3.7. Changes for the release are listed at
>> >>> http://www.mcs.anl.gov/petsc/documentation/changes/dev.html
>> >>>
>> >>>    Thanks
>> >>>
>> >>>    Barry
>> >>>
>> >>
>> >>
>>
>>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>

-- 
Jeff Hammond
jeff.science at gmail.com
http://jeffhammond.github.io/
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